The Emerging Role of the Gut Virome in Health and Inflammatory Bowel Disease: Challenges, Covariates and a Viral Imbalance

Abstract

Virome research is a rapidly growing area in the microbiome field that is increasingly associated with human diseases, such as inflammatory bowel disease (IBD). Although substantial progress has been made, major methodological challenges limit our understanding of the virota. In this review, we describe challenges that must be considered to accurately report the virome composition and the current knowledge on the virome in health and IBD. First, the description of the virome shows strong methodological biases related to wetlab (e.g., VLP enrichment) and bioinformatics approaches (viral identification and classification). Second, IBD patients show consistent viral imbalances characterized by a high relative abundance of phages belonging to the Caudovirales and a low relative abundance of phages belonging to the Microviridae. Simultaneously, a sporadic contraction of CrAss-like phages and a potential expansion of the lysogenic potential of the intestinal virome are observed. Finally, despite numerous studies that have conducted diversity analysis, it is difficult to draw firm conclusions due to methodological biases. Overall, we present the many methodological and environmental factors that influence the virome, its current consensus in health and IBD, and a contributing hypothesis called the "positive inflammatory feedback loop" that may play a role in the pathophysiology of IBD.

Keywords: IBD; bacteriophages; eukaryotic viruses; metagenomics; virome; virota.

Figure 2

Expansion of viral taxa over time. Development of ICTV taxonomy across multiple taxonomical hierarchies (Order, Family, Genus, and Species) from the first public record in 1971 until 2021. The white and grey-colored area on the plot represents the viral taxonomies in the pre-NGS and NGS era, respectively. The arrival of NGS technology coincides with an exponential increase in viral taxa, especially in the last decade. For example, the number of viral species rose from 2480 to 10,434 between 2011 and 2021, which is more than a quadrupling of the known species in only one decade. Adapted from ref. [153].

Figure 3

IBD patients possess an imbalanced intestinal virota and a dysregulated immune system under inflammatory conditions. (A) Environmental factors (e.g., smoking, stress, and Western diet) are believed to trigger intestinal inflammation in individuals predisposed to IBD. (B) This inflammatory condition is characterized by various viral imbalances compared to a healthy, non-inflamed gut. These imbalances include a high relative abundance of Caudovirales and a low relative abundance of Microviridae. In addition, the imbalances indicate a depletion of CrAss-like phages and possibly expansion of the lysogenic potential of the virome. (C) The altered intestinal virota is also associated with a dysregulated immune system. Here, breakdown of the mucus layer allows larger amounts of microbial antigens (e.g., viral antigens, flagellin) to stimulate Toll-like receptors in the intestinal mucosa, leading to the upregulation of proinflammatory signaling pathways and promotion of colitis. Red and blue arrows indicate the upregulated and downregulated pathways, respectively. Created with BioRender.com.

Figure 4

The hypothesis of phage-mediated lysis to sustain the positive inflammatory feedback loop in IBD patients. Intestinal inflammation stimulates the intestinal mucosa to produce stressors such as free radicals (e.g., ROS and NOS) (1) and triggers a stress response in the host bacteria called the “SOS response” (2). This response is a DNA damage response and leads to the induction of prophages (3), subsequent viral induction, and lysis of cells (4). Subsequently, pathogen-associated molecular patterns (e.g., LPS and peptidoglycan) are released, which in turn can stimulate the intestinal mucosa to produce further stressors, sustain the stress response in host bacteria, and thereby sustain the positive inflammatory feedback loop. Adapted from ref. [140] and created with BioRender.com.

Figure 1

Number of publications in microbiome and virome research. Number of publications were determined by querying the search term “Microbiome [TITLE/ABSTRACT]” and “Virome [TITLE/ABSTRACT]” on PubMed. In the year 2000, the first next-generation sequencing technology (e.g., massive-parallel sequencing) was launched, along with the first microbiome publication on PubMed. The first virome publication was published in 2003 on PubMed. In the last decade (2010–2021), the microbiome and virome research showed an exponential increase in publications with an average growth rate of 33.4% and 28.1% per year, respectively. Nonetheless, in 2021, virome studies constituted only a small fraction (3.54%) of the total microbiome publications.